Paper Citing NAMD - Abstract
Park, Sanghyun; Lau, Albert Y.; Roux, Benoit
Computing conformational free energy by deactivated morphing
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 134102, OCT 7 2008
Despite the significant advances in free-energy computations for biomolecules, there exists no general method to evaluate the free-energy difference between two conformations of a macromolecule that differ significantly from each other. A crucial ingredient of such a method is the ability to find a path between different conformations that allows an efficient computation of the free energy. In this paper, we introduce a method called "deactivated morphing," in which one conformation is morphed into another after the internal interactions are completely turned off. An important feature of this method is the (shameless) use of nonphysical paths, which makes the method robustly applicable to conformational changes of arbitrary complexity. (C) 2008 American Institute of Physics.
